October 12, 2017

Human pigmentation mega-study

A great new study on the genetics of human (including African) pigmentation. I would love to see a future study that would reconstruct what ancestral modern humans looked like pigmentation-wise, as this trait is tightly correlated with sun exposure (and thus latitude), and may thus pinpoint a narrow latitudinal zone where ancestral modern humans may have lived.

From a related story:
The most dramatic discovery concerned a gene known as MFSD12. Two mutations that decrease expression of this gene were found in high frequencies in people with the darkest skin. These variants arose about a half-million years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations.

Science 12 Oct 2017: eaan8433 DOI: 10.1126/science.aan8433

Loci associated with skin pigmentation identified in African populations

Nicholas G. Crawford et al.

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.